Yes. I do it all the time to fix up my MultiFormat ePubs from Fictionwise to read on the Kindle.

I will warn you that if your NCX happens to have some very minor and trivial errors in it, such as a superfluous </head> tag that normally shouldn't affect stuff besides the validator, KindleGen will merrily ignore your NCX and not even give you a warning message.

But otherwise it works just fine, except for the part where nested <navPoints> are accessible but invisible in the Kindle's location bar display.